Literature DB >> 18359830

Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms.

Mark R Liles1, Lynn L Williamson, Jitsupang Rodbumrer, Vigdis Torsvik, Robert M Goodman, Jo Handelsman.   

Abstract

We describe here an improved method for isolating, purifying, and cloning DNA from diverse soil microbiota. Soil microorganisms were extracted from soils and embedded and lysed within an agarose plug. Nucleases that copurified with the metagenomic DNA were removed by incubating plugs with a high-salt and -formamide solution. This method was used to construct large-insert soil metagenomic libraries.

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Year:  2008        PMID： 18359830      PMCID： PMC2394920          DOI： 10.1128/AEM.02630-07

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  15 in total

1.  Community level physiological profile of soil bacteria unaffected by extraction method.

Authors:  C Mayr; A Winding; N B Hendriksen
Journal:  J Microbiol Methods       Date:  1999-05       Impact factor: 2.363

2.  Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products.

Authors:  Sophie Courtois; Carmela M Cappellano; Maria Ball; Francois-Xavier Francou; Philippe Normand; Gérard Helynck; Asuncion Martinez; Steven J Kolvek; Joern Hopke; Marcia S Osburne; Paul R August; Renaud Nalin; Michel Guérineau; Pascale Jeannin; Pascal Simonet; Jean-Luc Pernodet
Journal:  Appl Environ Microbiol       Date:  2003-01       Impact factor: 4.792

3.  First insight into the genome of an uncultivated crenarchaeote from soil.

Authors:  Achim Quaiser; Torsten Ochsenreiter; Hans-Peter Klenk; Arnulf Kletzin; Alexander H Treusch; Guido Meurer; Jürgen Eck; Christoph W Sensen; Christa Schleper
Journal:  Environ Microbiol       Date:  2002-10       Impact factor: 5.491

4.  Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling.

Authors:  Marek K Sliwinski; Robert M Goodman
Journal:  Appl Environ Microbiol       Date:  2004-03       Impact factor: 4.792

5.  Isolation of High-molecular-weight DNA from Mammalian Cells Using Formamide.

Authors:  Joseph Sambrook; David W Russell
Journal:  CSH Protoc       Date:  2006-06-01

6.  Isolation of high molecular weight DNA from soil for cloning into BAC vectors.

Authors:  Andrew E Berry; Claudia Chiocchini; Tina Selby; Margherita Sosio; Elizabeth M H Wellington
Journal:  FEMS Microbiol Lett       Date:  2003-06-06       Impact factor: 2.742

7.  Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin.

Authors:  C S Jacobsen; O F Rasmussen
Journal:  Appl Environ Microbiol       Date:  1992-08       Impact factor: 4.792

8.  An improved approach for construction of bacterial artificial chromosome libraries.

Authors:  K Osoegawa; P Y Woon; B Zhao; E Frengen; M Tateno; J J Catanese; P J de Jong
Journal:  Genomics       Date:  1998-08-15       Impact factor: 5.736

9.  Molecular phylogeny of Archaea from soil.

Authors:  S B Bintrim; T J Donohue; J Handelsman; G P Roberts; R M Goodman
Journal:  Proc Natl Acad Sci U S A       Date:  1997-01-07       Impact factor: 11.205

10.  An ion-exchange based extraction method for the detection of salmonellas in soil.

Authors:  P E Turpin; K A Maycroft; C L Rowlands; E M Wellington
Journal:  J Appl Bacteriol       Date:  1993-02
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  23 in total

1.  Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study.

Authors:  Krishna M Singh; Viral B Ahir; Ajai K Tripathi; Umed V Ramani; Manisha Sajnani; Prakash G Koringa; Subhash Jakhesara; Paresh R Pandya; Dharamsi N Rank; Duggirala S Murty; Ramesh K Kothari; Chaitanya G Joshi
Journal:  Mol Biol Rep       Date:  2011-09-27       Impact factor: 2.316

2.  Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins.

Authors:  Justin J Donato; Luke A Moe; Brandon J Converse; Keith D Smart; Flora C Berklein; Patricia S McManus; Jo Handelsman
Journal:  Appl Environ Microbiol       Date:  2010-05-07       Impact factor: 4.792

3.  Size Does Matter: Application-driven Approaches for Soil Metagenomics.

Authors:  Kavita S Kakirde; Larissa C Parsley; Mark R Liles
Journal:  Soil Biol Biochem       Date:  2010-11-01       Impact factor: 7.609

Review 4.  Culture-independent discovery of natural products from soil metagenomes.

Authors:  Micah Katz; Bradley M Hover; Sean F Brady
Journal:  J Ind Microbiol Biotechnol       Date:  2015-11-19       Impact factor: 3.346

5.  Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples.

Authors:  Miguel I Uyaguari-Diaz; Jared R Slobodan; Matthew J Nesbitt; Matthew A Croxen; Judith Isaac-Renton; Natalie A Prystajecky; Patrick Tang
Journal:  J Vis Exp       Date:  2015-04-17       Impact factor: 1.355

6.  Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNA.

Authors:  Carlos Rios-Velazquez; Lynn L Williamson; Karen A Cloud-Hansen; Heather K Allen; Mathew D McMahon; Zakee L Sabree; Justin J Donato; Jo Handelsman
Journal:  J Microbiol Biol Educ       Date:  2011-12-01

7.  Novel Antibiotic Resistance Determinants from Agricultural Soil Exposed to Antibiotics Widely Used in Human Medicine and Animal Farming.

Authors:  Calvin Ho-Fung Lau; Kalene van Engelen; Stephen Gordon; Justin Renaud; Edward Topp
Journal:  Appl Environ Microbiol       Date:  2017-08-01       Impact factor: 4.792

8.  Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries.

Authors:  Kavita S Kakirde; Jadwiga Wild; Ronald Godiska; David A Mead; Andrew G Wiggins; Robert M Goodman; Waclaw Szybalski; Mark R Liles
Journal:  Gene       Date:  2010-11-26       Impact factor: 3.688

9.  Cloning large natural product gene clusters from the environment: piecing environmental DNA gene clusters back together with TAR.

Authors:  Jeffrey H Kim; Zhiyang Feng; John D Bauer; Dimitris Kallifidas; Paula Y Calle; Sean F Brady
Journal:  Biopolymers       Date:  2010-09       Impact factor: 2.505

Review 10.  Mining the metabiome: identifying novel natural products from microbial communities.

Authors:  Aleksandr Milshteyn; Jessica S Schneider; Sean F Brady
Journal:  Chem Biol       Date:  2014-09-18
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